RIP: Analysis of Residue Couplings

In these simulations, RIP perturbations are used to identify strong residue couplings. These couplings are particularly useful in identifying signficant tertiary interactions between pieces of secondary structure. I have a blog post for a longer explanation of how this can be used to identify allosteric modes in single domains.

Specifically, RIP is pplied with a a rotational temperature of 26K to a protein that has been pre-equilibrated to a nominal background temperature of 10K. A rotational temperature of 26K should reproduce the rotational velocities of sidechains at room temperature ~300K.

These perturbations identify pairs of residues that interact even in the interior of the protein.